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SYTL3 synaptotagmin like 3 [ Homo sapiens (human) ]

Gene ID: 94120, updated on 3-Apr-2024

Summary

Official Symbol
SYTL3provided by HGNC
Official Full Name
synaptotagmin like 3provided by HGNC
Primary source
HGNC:HGNC:15587
See related
Ensembl:ENSG00000164674 AllianceGenome:HGNC:15587
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SLP3
Summary
The protein encoded by this gene belongs to a family of peripheral membrane proteins that play a role in vesicular trafficking. This protein binds phospholipids in the presence of calcium ions. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in thyroid (RPKM 15.0), small intestine (RPKM 10.0) and 25 other tissues See more
Orthologs
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Genomic context

Location:
6q25.3
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (158644936..158764871)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (159886606..160010070)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (159071086..159185903)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene transmembrane protein 181 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:159030351-159030852 Neighboring gene TatD DNase domain containing 2 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159051575-159052076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159052077-159052576 Neighboring gene microRNA 7161 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:159053255-159053416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159065146-159066089 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17742 Neighboring gene dynein light chain Tctex-type 1 Neighboring gene MPRA-validated peak6273 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159128779-159129410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159129411-159130042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25360 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:159141094-159142293 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:159151193-159152392 Neighboring gene AMZ2 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159176343-159176927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:159180075-159180750 Neighboring gene Sharpr-MPRA regulatory region 4567 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:159192487-159192693 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:159193631-159194830 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:159205226-159206425 Neighboring gene microRNA 3918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25364 Neighboring gene ezrin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25368 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25369 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159245802-159246776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159256297-159256987 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159256988-159257678 Neighboring gene EZR antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159273679-159274204 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159274205-159274730 Neighboring gene uncharacterized LOC124901448 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159274731-159275254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25373 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159275781-159276305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:159276306-159276830 Neighboring gene oligosaccharyltransferase complex subunit pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Silencing of SLP3 by shRNA inhibits HIV-1 replication in Jurkat cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag Silencing the expression of SLP3 leads to a diffuse intracellular HIV-1 Gag staining pattern accompanied by a dramatic reduction in the association of Gag with the plasma membrane PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC105130, MGC118883, MGC118884, MGC118885

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium-dependent phospholipid binding IEA
Inferred from Electronic Annotation
more info
 
enables neurexin family protein binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables small GTPase binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in exocytic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
synaptotagmin-like protein 3
Names
exophilin-6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029794.2 RefSeqGene

    Range
    10120..124937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001009991.4NP_001009991.2  synaptotagmin-like protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001009991.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR and lacks two in-frame coding exons compared to variant 1. This results in a shorter isoform (2) compared to isoform 1. Variants 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AI674404, AK304191, AL567177, BC085612, DC394549
    Consensus CDS
    CCDS34563.1
    UniProtKB/TrEMBL
    B4DQA6
    Conserved Domains (3) summary
    cd04020
    Location:380542
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:239366
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cl22851
    Location:60108
    PHD_SF; PHD finger superfamily
  2. NM_001242384.2NP_001229313.1  synaptotagmin-like protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001229313.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1). Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AI674404, AK304191, AL567177, BC100830, DC394549
    Consensus CDS
    CCDS56458.1
    UniProtKB/Swiss-Prot
    Q496J4, Q496J6, Q4VX76, Q5U3B9
    UniProtKB/TrEMBL
    B4DQA6
    Related
    ENSP00000353631.4, ENST00000360448.8
    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  3. NM_001242394.2NP_001229323.1  synaptotagmin-like protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001229323.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate segment in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AI674404, AK304191, AL567177, BC100829, DC394549
    Consensus CDS
    CCDS56458.1
    UniProtKB/Swiss-Prot
    Q496J4, Q496J6, Q4VX76, Q5U3B9
    UniProtKB/TrEMBL
    B4DQA6
    Related
    ENSP00000483936.1, ENST00000611299.5
    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  4. NM_001242395.2NP_001229324.1  synaptotagmin-like protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001229324.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate segment in the 5' UTR and lacks two in-frame coding exons compared to variant 1. This results in a shorter isoform (2) compared to isoform 1. Variants 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AI674404, AK304191, AL567177, BC100828, DC394549
    Consensus CDS
    CCDS34563.1
    UniProtKB/TrEMBL
    B4DQA6
    Related
    ENSP00000356048.4, ENST00000367081.7
    Conserved Domains (3) summary
    cd04020
    Location:380542
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:239366
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cl22851
    Location:60108
    PHD_SF; PHD finger superfamily
  5. NM_001318745.2NP_001305674.1  synaptotagmin-like protein 3 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon compared to variant 1. The resulting isoform (3) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AI674404, AK055750, AK304191, AL589931, BC085612
    UniProtKB/TrEMBL
    B4E2A9
    Conserved Domains (2) summary
    cd04020
    Location:242404
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:101228
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    158644936..158764871
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715606.4XP_006715669.1  synaptotagmin-like protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006715669.1

    UniProtKB/Swiss-Prot
    Q496J4, Q496J6, Q4VX76, Q5U3B9
    UniProtKB/TrEMBL
    B4DQA6
    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  2. XM_047419556.1XP_047275512.1  synaptotagmin-like protein 3 isoform X2

  3. XM_011536254.3XP_011534556.1  synaptotagmin-like protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011534556.1

    UniProtKB/Swiss-Prot
    Q496J4, Q496J6, Q4VX76, Q5U3B9
    UniProtKB/TrEMBL
    B4DQA6
    Conserved Domains (4) summary
    cd04020
    Location:448610
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:307434
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
    cd15765
    Location:60108
    FYVE_Slp3; FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins
    cl22851
    Location:8123
    PHD_SF; PHD finger superfamily
  4. XM_006715611.4XP_006715674.1  synaptotagmin-like protein 3 isoform X4

    See identical proteins and their annotated locations for XP_006715674.1

    UniProtKB/TrEMBL
    B4E2A9
    Conserved Domains (2) summary
    cd04020
    Location:242404
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:101228
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
  5. XM_047419560.1XP_047275516.1  synaptotagmin-like protein 3 isoform X4

  6. XM_047419552.1XP_047275508.1  synaptotagmin-like protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q496J4, Q496J6, Q4VX76, Q5U3B9
  7. XM_047419557.1XP_047275513.1  synaptotagmin-like protein 3 isoform X2

  8. XM_047419553.1XP_047275509.1  synaptotagmin-like protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q496J4, Q496J6, Q4VX76, Q5U3B9
  9. XM_047419550.1XP_047275506.1  synaptotagmin-like protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q496J4, Q496J6, Q4VX76, Q5U3B9
  10. XM_047419554.1XP_047275510.1  synaptotagmin-like protein 3 isoform X2

  11. XM_047419549.1XP_047275505.1  synaptotagmin-like protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q496J4, Q496J6, Q4VX76, Q5U3B9
  12. XM_047419555.1XP_047275511.1  synaptotagmin-like protein 3 isoform X2

  13. XM_047419558.1XP_047275514.1  synaptotagmin-like protein 3 isoform X2

  14. XM_047419551.1XP_047275507.1  synaptotagmin-like protein 3 isoform X1

    UniProtKB/Swiss-Prot
    Q496J4, Q496J6, Q4VX76, Q5U3B9
  15. XM_047419561.1XP_047275517.1  synaptotagmin-like protein 3 isoform X4

  16. XM_017011499.2XP_016866988.1  synaptotagmin-like protein 3 isoform X6

  17. XM_017011496.2XP_016866985.1  synaptotagmin-like protein 3 isoform X4

    UniProtKB/TrEMBL
    B4E2A9
    Conserved Domains (2) summary
    cd04020
    Location:242404
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:101228
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
  18. XM_047419562.1XP_047275518.1  synaptotagmin-like protein 3 isoform X5

  19. XM_047419559.1XP_047275515.1  synaptotagmin-like protein 3 isoform X4

  20. XM_005267222.5XP_005267279.1  synaptotagmin-like protein 3 isoform X4

    See identical proteins and their annotated locations for XP_005267279.1

    UniProtKB/TrEMBL
    B4E2A9
    Conserved Domains (2) summary
    cd04020
    Location:242404
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:101228
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3
  21. XM_011536255.3XP_011534557.1  synaptotagmin-like protein 3 isoform X3

    Conserved Domains (2) summary
    cd04020
    Location:247409
    C2B_SLP_1-2-3-4; C2 domain second repeat present in Synaptotagmin-like proteins 1-4
    cd08392
    Location:106233
    C2A_SLP-3; C2 domain first repeat present in Synaptotagmin-like protein 3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    159886606..160010070
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356804.1XP_054212779.1  synaptotagmin-like protein 3 isoform X1

  2. XM_054356801.1XP_054212776.1  synaptotagmin-like protein 3 isoform X1

  3. XM_054356814.1XP_054212789.1  synaptotagmin-like protein 3 isoform X2

  4. XM_054356824.1XP_054212799.1  synaptotagmin-like protein 3 isoform X6

  5. XM_054356806.1XP_054212781.1  synaptotagmin-like protein 3 isoform X2

  6. XM_054356793.1XP_054212768.1  synaptotagmin-like protein 3 isoform X1

  7. XM_054356794.1XP_054212769.1  synaptotagmin-like protein 3 isoform X1

  8. XM_054356811.1XP_054212786.1  synaptotagmin-like protein 3 isoform X2

  9. XM_054356798.1XP_054212773.1  synaptotagmin-like protein 3 isoform X1

  10. XM_054356797.1XP_054212772.1  synaptotagmin-like protein 3 isoform X1

  11. XM_054356809.1XP_054212784.1  synaptotagmin-like protein 3 isoform X2

  12. XM_054356803.1XP_054212778.1  synaptotagmin-like protein 3 isoform X1

  13. XM_054356807.1XP_054212782.1  synaptotagmin-like protein 3 isoform X2

  14. XM_054356800.1XP_054212775.1  synaptotagmin-like protein 3 isoform X1

  15. XM_054356812.1XP_054212787.1  synaptotagmin-like protein 3 isoform X2

  16. XM_054356819.1XP_054212794.1  synaptotagmin-like protein 3 isoform X4

  17. XM_054356818.1XP_054212793.1  synaptotagmin-like protein 3 isoform X4

  18. XM_054356802.1XP_054212777.1  synaptotagmin-like protein 3 isoform X1

  19. XM_054356796.1XP_054212771.1  synaptotagmin-like protein 3 isoform X1

  20. XM_054356808.1XP_054212783.1  synaptotagmin-like protein 3 isoform X2

  21. XM_054356795.1XP_054212770.1  synaptotagmin-like protein 3 isoform X1

  22. XM_054356810.1XP_054212785.1  synaptotagmin-like protein 3 isoform X2

  23. XM_054356813.1XP_054212788.1  synaptotagmin-like protein 3 isoform X2

  24. XM_054356799.1XP_054212774.1  synaptotagmin-like protein 3 isoform X1

  25. XM_054356805.1XP_054212780.1  synaptotagmin-like protein 3 isoform X1

  26. XM_054356822.1XP_054212797.1  synaptotagmin-like protein 3 isoform X4

  27. XM_054356821.1XP_054212796.1  synaptotagmin-like protein 3 isoform X4

  28. XM_054356820.1XP_054212795.1  synaptotagmin-like protein 3 isoform X4

  29. XM_054356823.1XP_054212798.1  synaptotagmin-like protein 3 isoform X4

  30. XM_054356816.1XP_054212791.1  synaptotagmin-like protein 3 isoform X4

  31. XM_054356817.1XP_054212792.1  synaptotagmin-like protein 3 isoform X4

  32. XM_054356815.1XP_054212790.1  synaptotagmin-like protein 3 isoform X3